Vermont Yankee's state permit to send millions of gallons of heated water into the Connecticut River every day expired in March 2006. But because the company applied for a new permit on time, the old permit has been extended indefinitely.

That leaves Vermonters like Deen, an avid fisherman, state representative from Westminster and member of the Connecticut River Watershed Council, stuck in a holding pattern. No one can appeal the permit until there is a permit to appeal.

"They have a zombie permit and we're stuck in limbo," Deen said Friday in his House Fish, Wildlife and Water Resources Committee room in the Statehouse.

No matter what happens to Vermont Yankee in the next several years – whether it closes in March 2012 as scheduled or continues operating for 20 years after that – a potential legislative and legal battle looms over the issue of the higher-than-average temperature of the water the plant emits.

Vermont Yankee pulls in water from the nearby Connecticut River – up to 543 million gallons a day – and uses it to cool its system instead of relying on the facility's cooling towers, a process that is more expensive and uses some of the electricity generated by the plant. In the summer, this water can be as hot as 100 degrees when it comes out of the plant.

But that water coming back into the river is at a higher temperature than the water taken in – sometimes as much as 5 or 6 degrees warmer. Environmentalists who have worked to protect the river and its wildlife say that slight rise in the water temperature can cause havoc for some of the species living and breeding there.

Deen points to the American shad as a chief example. The species usually lives at sea but comes up the river to spawn annually. But the American shad will breed only at certain temperatures, Deen said, and with the hotter water heating up the river he worries that this change in habitat could be killing them or driving them away.

In 1992 – one year after Vermont Yankee began increasing the temperature of the water from 2 degrees above normal to 5 degrees above – the nearby Vernon dam counted about 37,000 American shad swimming by. The 2009 count was 19.

Vermont Yankee's request several years ago to amend its water discharge permit from the Vermont Agency of Natural Resources landed the company in court, its chief opponents being the Connecticut River Watershed Council and Vermont Law School, which represented the tiny organization pro bono.

Last winter, the Vermont Supreme Court upheld an earlier decision by an Environmental Court judge to allow Vermont Yankee to increase the temperature of the Connecticut River by another 1 degree in the summer, ending a nearly three-year legal battle over that change.

But since that December decision, the issue has gone silent. Opponents of Vermont Yankee's water discharge plans have been waiting for the ANR to approve, deny or put conditions on the permit application. It's an application that was made more than four years ago.

Vermont Yankee spokesman Rob Williams said the company filed for its new five-year permit on time in September 2005. Because of that, the prior permit, which expired March 31, 2006, was extended until a decision on the new permit is issued. This is standard procedure, Williams said.

But David Mears, a Vermont Law School professor who represented the watershed council in the legal challenge, said that essentially puts opponents of the water discharge plan in a holding pattern. They can't legally challenge a permit until one is actually issued, he said.

"I know these ANR processes take time," he said. "But right now we are being denied the opportunity to challenge the permit."

Justin Johnson, the commissioner of the Vermont Department of Environmental Conservation, a division of the resources agency, said it usually does not take this long for the state to issue a decision on permits such as these – but he stressed that Vermont Yankee's is a unique and complicated case.

"I think we could call this a nonstandard case," Johnson said last week. "There are a lot of issues around the increased thermal discharge that we need to look at."

Johnson said the scope of the Vermont Yankee permit – applications for similar discharge permits typically come from much smaller operations – requires that a host of studies be conducted to determine the effects of the increased temperature on the river and its wildlife. Meanwhile, the long legal battle over the amended permit put much of this process on hold, he said.

"Has this taken longer than I would like?" Johnson said. "Yeah, it has. But the thermal issues are complicated and we need to reach out to people who have expertise in this area. We're making sure we get this right."

Deen said agency staff have "been briefed about our concerns." In the meantime, the watershed council has been researching and writing position papers, he said. It has also designed some trial programs to test the effects of warmer water on aquatic wildlife, which the group is willing to share with the state.

Deen said he doesn't hold a grudge against the Agency of Natural Resources for the speed of this permit process. Staff right now are assisting on the tritium leak investigation at the plant, he said, and have been the focus of repeated budget cuts throughout the years, limiting the resources available to work quickly on big cases.

"They've had a number of personnel cuts since the '80s," he said. "They've always been the stepchild of state government spending."

One of the things that Deen has asked the agency is whether last month's vote by the Vermont Senate to effectively shut down the nuclear power plant in two years has any bearing on the permit application process. He hasn't heard back.

"That's one of the things we're looking at," Johnson said.

Deen said the watershed council's relationship with the state is not adversarial.

"I'm not necessarily assuming that they will approve this permit," Deen said. "I'm not saying they will reject it, but it's always a possibility that they put some real conditions on the permit, limiting this discharge."

He said it's never been the council's goal to shut down Vermont Yankee.

"That's not our mission," he said. "We're focused on the river. Once our issues are resolved, we go away."